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PSYC20006 -Theme 4: Genetics (W11-12) > W11 - Genetics 1 > Flashcards

W11 - Genetics 1 Flashcards

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1
Q

What are the building blocks of genetic code.

What are proteins, what determines their function, and what are their building blocks.

A

Nucleotides or bases:

Building blocks of the genetic code

  • Adenine (A); Cytosine (C); Thymine (T); Guanine (G)

Amino Acids

Building blocks of proteins

  • Represented by specific sequence of three bases
    • Codons
  • Function of a protein is determined by its structure
  • Structure of a protein is determined by its sequence of amino acids
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2
Q

How many bases are there in the whole human genome and how many genes code for protein?

A

Bases:

3 billion bases

Genes that code for protein:

20–25 thousand genes

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3
Q

What is the helix of DNA. What do they carry?

A

Double-stranded. The two strands carry redundant information.

Each base has a partner on the other strand

  • Cytosine pairs with Guanine (C–G)
  • Adenine pairs with Thymine (A–T)
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4
Q

How is DNA bundled. What is the human karyotype comprise of?

A

DNA is bundled in chromosomes

  • The human karyotype comprises 46 chromosomes:
    • 22 pairs of autosomal chromosomes (1–22)
    • Two sex chromosomes (XX or XY)
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5
Q

What determines the structure of protein

A

Structure of a protein is determined by its sequence of amino acids

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6
Q

What happens when we change a single bases in a codon. What is the caveat

A

Changing Bases

  • Changes the amino acid
  • Change structure of protein
  • Change function of protein

Caveat

Not necessarily, as each amino acid might has multiple possible codons

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7
Q

What is a single-nucleotide polymorphism (SNP). What are the different bases called?

A

SNP

  • Position on the genome at which the bases (nucleotide) differs between individual
  • The two alleles of a SNP are the alternative bases
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8
Q

What determines a person’s genotype at SNP?

A

Determined by the two alleles on the two copies of the chromosome

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9
Q

What is phenotype. What kinds are there?

A

Phenotype is the presence, absence or value of a trait of interest

E.g.

  • Psychological diagnosis (binary)
  • Parenting style (categorical)
  • IQ (quantitative)
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10
Q

What are the 5 genetic variants

A
  1. SNP
  2. Insertion–deletion
  3. Block substitution
  4. Inversion
  5. Copy number
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11
Q

Genetic Variant 0

A

SNP: Single Base differ

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12
Q

Genetic Variant 1

A

Insertion–deletion variant

  • Bases added or missing
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13
Q

Genetic Variant 2

A

Block substitution

  • Multiple bases substituted
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14
Q

Genetic Variant 3

A

Inversion variant

  • Bases replaced with reversed sequence from other strand
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15
Q

Genetic Variant 4

A

Copy-number variant

  • Sequence of bases repeated one or more times
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16
Q

What is the difference between mutation and polymorphism

A

Mutation:

Rare (<1% allele of population)

Polymorphism:

Common (1%/>1% allele of population)

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17
Q

Male vs Female chromosome. What is the extra step

A

Female: XX

Male: XY

  • In females, to avoid excess X-chromosome protein, one copy of X in each cell is silence/inactivate
    • This process is random in all mammals
18
Q

How does one copy of X get inactivated

A
  • XIST gene
    • RNA transcript
      • Coats one chromosome to be inactivated as a Barr body
  • TSIX gene, on other chromosome
    • RNA transcript
      • Suppresses transcription of XIST
  • TSIX antisense partner of XIST
    • Encoded by same stretch of DNA; transcribed in opposite directions
19
Q

What is gene equation

A

P = G + E + GxE + 2cov(G,E)

  • P: Phenotype Variance
  • G: Geneotype Variance
  • E: Environment Variance
  • GxE: Variance from gene–environment interactions
  • 2cov(G,E): Covariance between genes and environment
20
Q

What is the heritability equation

A

h2 = G / P

Therefore, proportion of variance in the phenotype that can be attributed to variance from genes

21
Q

Define heritability

A

Heritability is the proportion of the phenotypic variance due to genetic causes

22
Q

What kind of measurement is heritability based on?

A
  • Local measurement
    • Valid for specific population at a specific time
      • Depends on the amount of genetic and environmental variation present in the population
      • Cannot generalise heritability across populations…
23
Q

Hertiability of some disorders

A

High

  • Autism
  • ADHD
  • Schizophrenia
  • Biopolar
  • OCD

Low

  • MDD
  • Anxiety
  • Alcohol
  • Eating disorders
    *
24
Q

How do we measure heritability pre-molecular genetics. What fact do we make use of/

A

Genetic epidemiology

  • Related individuals share a predictable amount of genetic material
25
Q

Example of genetic epidemiology

A

Twin studies: Concordance rates

  • Higher concordnace in MZ (identical genetics) than DZ (half genetics) suggests genetics component
26
Q

What are models of inheritance

A
  • Dominant vs Recessive
  • Autosomal vs X-linked
27
Q

Dominant vs recessive

A

Dominant traits

Mutation on one copy of chromosome for expression of the phenotype

Recessive traits

Mutation on both copies (or only copy) of the chromosome

28
Q

Autosomal vs X-linked*

A
  • Autosomal traits are carried on the autosomal chromosomes (1–22)
  • X-linked traits are carried on the X chromosome
29
Q

How can we infer modes of inheritance

A

Modes of inheritance can be inferred from a pedigree chart

  • Black = Affected
  • White = Unaffected
  • Circle = Female
  • Square = Male
  • Slash = Deceased
30
Q

Pedigree Chart Reading

A

See Picture

Main Ideas

Dominant

  • Cannot skip
  • 2 Unaffected Parents cannot have affected offspring

Recessive

  • Can skip
  • 2 Affected parents cannot have unaffected offspring

X-Linked

  • Cannot transfer father to son
  • (Recessive) More common in males
  • (X-Linked + Dominant) Daughter of affected father must be affected, but father of affected daughter may not be affected
  • (X-Linked + Recessive) Father of affected daughter must be affected
31
Q

What is an example of a mongenic disorder

A

Fragile-X (Originated from single gene)

32
Q

What is the gene alteration of fragile-X

A

Copy-number variant

  • in 5′-untranslated region (contains promotor region where transcribing begins) of gene FMR1
    • FMR1 essential for synaptic plasticity/learning
  • expanded CCG sequence triggers methlyation
    • _​_constricts X chromosome, causing ‘fragile’ appearance
    • methyldated promotor region prevents transcription of the gene
33
Q

What are Polygenic disorders. Are they common?

A

Many genes with small contribution.

Monogenic disorders (Fragile-X) are the exception to the rule in behavioural and psychiatric genetics: No single gene for schizophrenia, autism, bipolar disorder, depression or anxiety

34
Q

What does GWAS do

A

Genome-wide association studies:

  • Examine statistical association between a phenotype and many SNP markers throughout the genome
    • 500,000 - 2,000,000 markers
35
Q

What is linkage disequilibrium (LD) and what does it allow us to do. What can chromosomes be thought of

A
  • Association of alleles at different loci in a population is non-random
    • _​_Chromosomes are mosaics (inherited together in chunks), and hence many variants are correlated
  • Allows us to observe indirect associations
36
Q

What is a direct association and indirect association in GWAS

A

Direct association

  • Phenotype has a functional association with a genotyped (measured) SNP

Indirect association

  • Phenotype has a functional association with a non-genotyped SNP that is in LD with a genotyped SNP
37
Q

What is allelic dosage model and allelic association model

A

Allelic dosage model

Quantitative traits

Is there a statistical association between the phenotypic measurement and the number of copies of the minor allele?

Allelic association model

Categorical and Binary traits

Is one of the two alternative alleles statistically
over-represented in a phenotypic group?

38
Q

What summarises the results of all GWAS tests of association

A

Manhattan plot

  • Each point represents outcome of test for ONE snp
    • x-axis
      • Physical location on genome and within a chromosone
    • y-axis
      • Transformed p value
      • Lower p value = higher on axis = stronger association
39
Q

What are the thresholds for significance in GWAS

A

Stringent, due to multiple comparisions increasing type 1 error

  • a < 5 x 10^-8
    • Corresponds to Bonferroni correction for ~1 million independent (uncorrelated) tests
40
Q

What predicts genotypes at nongenotyped SNPs

A

Imputation

  • Relies on data from a reference panel of individuals genotyped at high density
  • Applies patterns of linkage disequilibrium
    discovered in the reference panel
41
Q

What is the term defining “extent to which a sequence is
maintained across species”

A

Conservation

  • High conservation = Important function for evolution
42
Q

What helps to define the region likely to contain the
functional variant in a SNP (Other than LD)

A
  • Genetic distance
  • Recombination rate
    • Frequency with which two markers are inherited together

PSYC20006 -Theme 4: Genetics (W11-12) (3 decks)

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